#!/bin/bash

  # Define QUEUE in RNS space ... not local file system space
#QUEUE=/home/xsede.org/prodhan/queues/new-jsdl-queue
QUEUE=/resources/CCC/queues/NormalQueue
INCOUNT=0
OUTCOUNT=0
# HOSTNAME=`hostname`

# Modify the GENII_ROOT to point to your mounted home grid home
# GENII_ROOT=/home/xsede.org/prodhan/

GPATHS_IN=()
IN_NAME=()
GPATHS_OUT=()
OUT_NAME=()
# BLOCK_SIZE=1

preprocessing(){
  file=$1
  while IFS=, read -r lpath gpath name
  do
    if [ ! -z "$lpath" ]
    then
      fastgrid cp local:$lpath $gpath
    fi
    GPATHS_IN[INCOUNT]=$gpath 
    IN_NAME[INCOUNT]=$name
    INCOUNT=$(( $INCOUNT + 1 ))
  done <"$file" 
  
  file1=$2
  while IFS=, read -r lpath_o gpath_o name_o 
  do
    GPATHS_OUT[OUTCOUNT]=$gpath_o 
    OUT_NAME[OUTCOUNT]=$name_o
    OUTCOUNT=$(( $OUTCOUNT + 1 ))
  done <"$file1"
    
}


run_jobs() {
# ***************************************************************
# param $1 is the "name" of the test directory
# param $2 is the number of iterations
# param $3 is the jsdl file to modify


echo "generating jobs"
i=0
temp_file=$(mktemp)

while (( $i < $2 ))
do
  echo "Starting $i"
  cat $3 >tmp
  
  echo $INCOUNT $OUTCOUNT
  k=0
  for ((k=0;k<INCOUNT;k++))
  do
    input=INPUT$k
    inputfile=INPUTFILENAME$k
    echo replacing $input with ${GPATHS_IN[k]} and $inputfile with ${IN_NAME[k]}
  	sed -i "s|$inputfile|${IN_NAME[k]}|;s|$input|${GPATHS_IN[k]}|" tmp
 	done
  
  l=0
  for ((l=0;l<OUTCOUNT;l++))
  do
    output=OUTPUT$l
    outputfile=OUTPUTFILENAME$l
    echo replacing ${output} with ${GPATHS_OUT[l]} and ${outputfile} ${OUT_NAME[l]}
  	sed -i "s|${output}|${GPATHS_OUT[l]}|;s|${outputfile}|${OUT_NAME[l]}|" tmp 
 	done  
  
  cat tmp >${temp_file}
  
  i=$(( $i + 1 ))
  # m=$((i%BLOCK_SIZE))
  # if ((m == 0)); then
  #	 echo "hit the mod"
  #   echo "transfering jobs to queue"
  PWD=`pwd`
  echo "fastgrid qsub ${QUEUE} "local:"${temp_file}"
  fastgrid qsub ${QUEUE} "local:"${temp_file}
  echo "job $i submitted"
  #fi
done
#echo "jobs submitted"

rm ${temp_file}
rm tmp
}

monitor () {
# Now monitor the jobs
# ***************************************************************
# param $1 is the number of iterations


sleep 10
# First, get my session cert EPI
my_cert_epi=`fastgrid whoami | tail --lines 2 | head --lines 1 | grep Cert | awk '{ print $2 }' | sed 's/\"//g'`
echo $my_cert_epi
echo "waiting for " $1 " to complete" 
declare -i completed=0
declare -i count=0
while (( $completed<$1 ))
do
	sleep 30
# First get a list of completed jobs
	fastgrid qlist $QUEUE  > $$.qlist
	cat $$.qlist | grep $my_cert_epi | grep "FINISHED" | awk '{print $1 }'  > $$.tmp
	cat $$.tmp
	if [ -s $$.tmp ]
	then
# now clean them up
		xargs -a $$.tmp grid qcomplete $QUEUE
# add the count to the number completed
		let count=0
		count=`cat $$.tmp | wc -l`
		let completed=completed+count
	fi

	
	echo "There are " $completed " completed"
done
}

#if [ $# -ne 2 ]
#then
#	echo "USAGE:  $0 <number-of-times> <jsdl-file>"
#	exit 1
#fi

while getopts i:o:j:n:m: option
do
    case "${option}"
    in
            i) inputfile=${OPTARG};;
            o) outputfile=${OPTARG};;
            j) jsdlfile=${OPTARG};;
            n) numberofjobs=${OPTARG};;
            m) monitor=$OPTARG;;
    esac
done


if [ -z "$jsdlfile" ]
then
    echo "No JSDL file provided. So exiting"
    exit 1
fi

# Do any pre-processig here
if [ ! -z "$inputfile" ] || [ ! -z "$outputfile" ]
then
    preprocessing $inputfile $outputfile
fi

if [ -z "$numberofjobs" ]
then
    echo "Since # of Jobs not specified, submitting 1 job"
    numberofjobs=1
fi

run_jobs test $numberofjobs $jsdlfile
if [ -z "$monitor" ] || [ ! $monitor -eq "True" ]
then
    echo "monitor flag not set. So exiting"
    exit 0
fi 
monitor $numberofjobs
# Do the post-processing here